Hi Maryam,

You can easily align two proteins in Pymol to compare their structures. Read 
both protein structures into the same window under the action option, choose 
align and select which one you want. E.g align to molecule (via alpha carbons)
Hope this is what you wanted


From: mtaraz...@chem.ucsb.edu <mtaraz...@chem.ucsb.edu>
Sent: Saturday, 23 May 2020 11:18 am
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Structure allignmnet in Pymol

Dear All,
I am a new user in PyMoL and I have a question regarding the structure 
alignment in PyMOL.
I have a protein that its crystal structure is not known. So I used "Modeller" 
software to predict the structure of its closet hit. ( I can easily visualize 
the structure of the closet hit in PyMOL)
Now I want to visualize the structure of initial protein (the one that its  
crystal structure was not known) based on the structure of its closest hit.
I tried that with "Chimera" software using structure alignment. I would like to 
know if PyMoL is able to do that?
Any suggestion would greatly be appreciated.
Best regards

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